Intron features of key functional genes mediating nitrogen metabolism in marine phytoplankton

Introns are widespread and variable in eukaryotic genomes. Although their histories and functions, or even whether all of them have any function, remain largely unknown, analysis of intron sequences and genomic contexts may shed light on the evolutionary history of genes and organisms. The number and frequency of introns vary widely in the small number of published genomes of protists and algae suggesting that the same is true of the vast diversity of protists and algae that remain uncultivated. The objective of this study were to investigate introns in sequences of functional genes of phytoplankton, both in published genomes and in sequences obtained from environmental clone libraries. We examined the introns of the genes involved in nitrogen uptake and assimilation pathways in the genome sequences of cultivated phytoplankton as well as in environmental clone libraries of nitrate reductases (NR), nitrite reductase (NiR), nitrate transporter (Nrt2) and ammonium transporter (AMT) genes constructed from pelagic phytoplankton communities in Monterey Bay (CA, USA) and Onslow Bay (NC, USA). Here we describe the most extensive set to date of intron sequences from uncultivated marine algae and report important differences for diatom vs. non-diatom sequences. The majority of the introns in NR, NiR, Nrt2 and AMT from cultured phytoplankton and environmental libraries showed canonical splice patterns. Introns found in diatom-like NR environmental libraries had lower GC content than the respective exons. The green algal-like NR and Nrt2 environmental sequences had introns and exons of much more similar GC content, and both higher than in diatoms. These patterns suggest a different evolutionary history and recent acquisition of diatom introns compared to other algae.

► Introns of key nitrogen metabolizing genes in cultured phytoplankton and environmental libraries investigated.
► Majority of the introns in NR, NiR, Nrt2 and AMT genes showed canonical splice patterns.
► Introns found in diatom-like NR environmental libraries had lower GC content than the respective exons.
► Green algal-like NR and Nrt2 environmental sequences had introns and exons of similar GC content, higher than in diatoms.
► Patterns suggest a different evolutionary history and recent acquisition of diatom introns compared to other algae.